Contacts of the helix formed by residues 298 - 305 (chain A) in PDB entry 4JU5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A PHE* 4.1 5.1 + - - -
291A ILE* 3.6 26.6 - - + +
292A ASP* 2.9 30.9 + - - +
293A SER 6.1 0.2 - - - -
295A HIS* 2.9 22.6 + - - +
297A ASP* 1.3 84.3 + - - +
299A GLN* 1.3 62.8 + - - +
300A ARG 3.3 3.1 - - - -
301A ILE* 3.3 12.7 + - + +
302A LEU* 3.2 31.7 + - + +
300B ARG* 3.5 27.6 + - - +
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A SER 5.5 1.1 - - - -
294A ASP 5.1 2.3 - - - +
295A HIS 4.0 2.8 + - - +
296A THR* 3.0 40.5 + - - +
297A ASP 3.5 0.8 - - - -
298A ASN* 1.3 76.9 - - - +
300A ARG* 1.3 63.0 + - - +
302A LEU* 3.3 25.4 + - - +
303A GLU* 3.1 38.4 + - - +
309A LYS* 4.3 25.9 - - - +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ASP 5.1 1.0 + - - -
298A ASN 3.3 0.6 - - - -
299A GLN* 1.3 78.9 - - - +
301A ILE* 1.3 57.9 + - - +
303A GLU* 3.4 23.8 + - - +
304A PHE* 2.9 27.5 + - - +
240B PHE* 3.5 33.4 + - - -
241B THR* 4.2 5.8 - - - +
242B GLU* 4.3 17.8 + - - +
295B HIS* 5.5 2.6 - - - -
297B ASP* 3.0 40.5 + - - +
298B ASN* 2.6 31.4 + - - +
300B ARG* 4.6 13.0 - - + -
301B ILE* 3.4 22.1 - - + +
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PHE* 3.4 39.0 - - + -
260A PHE* 4.0 14.6 - - + -
291A ILE* 4.1 13.5 - - + -
298A ASN* 3.3 16.7 + - + +
300A ARG* 1.3 75.6 - - - +
302A LEU* 1.3 66.1 + - + +
304A PHE* 3.4 6.0 + - - +
305A PHE* 3.1 49.2 + - + -
300B ARG* 3.5 32.5 - - + +
301B ILE* 5.0 4.5 - - + +
304B PHE* 3.8 16.4 - - + -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A PHE* 3.7 32.5 - - + -
291A ILE* 5.9 0.4 - - + -
292A ASP 5.5 0.2 - - - -
293A SER* 3.9 34.5 - - - +
298A ASN* 3.2 29.5 + - + +
299A GLN* 3.4 27.4 - - - +
301A ILE* 1.3 76.4 - - + +
303A GLU* 1.3 57.6 + - + +
305A PHE* 3.1 9.5 + - - -
306A GLY 3.2 0.2 + - - -
307A LEU* 2.8 45.2 + - + +
308A LYS* 4.4 1.8 - - - -
309A LYS* 4.0 26.2 - - - +
312A CYS* 4.9 1.3 - - - -
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A GLN* 3.1 27.9 + - - +
300A ARG* 3.5 36.2 + - - +
302A LEU* 1.3 72.4 - - + +
304A PHE* 1.3 67.1 + - - +
306A GLY* 2.9 14.8 + - - +
307A LEU 4.4 7.9 - - - +
240B PHE* 4.7 1.7 - - + -
241B THR 5.2 0.2 - - - +
242B GLU* 3.7 33.8 - - - +
245B ALA* 3.3 30.1 - - + +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ARG 2.9 18.0 + - - +
301A ILE* 3.5 9.6 - - - +
302A LEU 3.4 0.2 - - - -
303A GLU* 1.3 75.5 - - - +
305A PHE* 1.3 86.1 + + + +
306A GLY 3.6 1.6 + - - -
240B PHE* 3.7 30.1 - + + -
245B ALA 5.1 2.9 - - - +
248B ILE* 5.6 5.0 - - - +
249B PHE* 5.1 4.5 + - - +
256B HIS* 6.0 1.3 - - - -
258B LEU* 3.7 37.2 - - + -
289B ILE* 5.9 4.5 - - + -
291B ILE* 4.7 6.1 - - + -
301B ILE* 4.0 21.3 - - + -
304B PHE* 5.9 0.2 - + - -
305B PHE* 3.8 22.2 - + - -
318B ILE* 4.2 17.0 - - + -
320B LEU* 5.2 10.5 - - + +
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LEU* 3.8 23.6 - - + -
260A PHE* 3.9 13.5 - + + -
301A ILE* 3.1 30.6 + - + +
302A LEU 3.1 3.7 + - - +
303A GLU 3.1 1.0 - - - -
304A PHE* 1.3 100.5 - + - +
306A GLY* 1.3 64.1 + - - +
307A LEU* 3.3 12.5 + - + +
316A ARG* 3.7 46.5 + - + -
318A ILE* 4.2 13.2 - - + -
249B PHE* 4.5 7.4 - - - +
304B PHE* 3.9 23.1 - + - -
320B LEU* 3.7 30.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il